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Yorodumi- PDB-4c13: x-ray crystal structure of Staphylococcus aureus MurE with UDP-Mu... -
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-Basic information
Entry | Database: PDB / ID: 4c13 | |||||||||
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Title | x-ray crystal structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys | |||||||||
Components | UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE | |||||||||
Keywords | LIGASE / MURE | |||||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Ruane, K.M. / Roper, D.I. / Fulop, V. / Barreteau, H. / Boniface, A. / Dementin, S. / Blanot, D. / Mengin-Lecreulx, D. / Gobec, S. / Dessen, A. ...Ruane, K.M. / Roper, D.I. / Fulop, V. / Barreteau, H. / Boniface, A. / Dementin, S. / Blanot, D. / Mengin-Lecreulx, D. / Gobec, S. / Dessen, A. / Dowson, C.G. / Lloyd, A.J. | |||||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy. Authors: Wang, L. / Shao, X. / Zhong, T. / Wu, Y. / Xu, A. / Sun, X. / Gao, H. / Liu, Y. / Lan, T. / Tong, Y. / Tao, X. / Du, W. / Wang, W. / Chen, Y. / Li, T. / Meng, X. / Deng, H. / Yang, B. / He, ...Authors: Wang, L. / Shao, X. / Zhong, T. / Wu, Y. / Xu, A. / Sun, X. / Gao, H. / Liu, Y. / Lan, T. / Tong, Y. / Tao, X. / Du, W. / Wang, W. / Chen, Y. / Li, T. / Meng, X. / Deng, H. / Yang, B. / He, Q. / Ying, M. / Rao, Y. #1: Journal: J.Biol.Chem. / Year: 2013 Title: Specificity Determinants for Lysine Incorporation in Staphylococcus Aureus Peptidoglycan as Revealed by the Structure of a Mure Enzyme Ternary Complex. Authors: Ruane, K.M. / Lloyd, A.J. / Fulop, V. / Dowson, C.G. / Barreteau, H. / Boniface, A. / Dementin, S. / Blanot, D. / Mengin-Lecreulx, D. / Gobec, S. / Dessen, A. / Roper, D.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c13.cif.gz | 198.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c13.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c13_validation.pdf.gz | 707.5 KB | Display | wwPDB validaton report |
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Full document | 4c13_full_validation.pdf.gz | 711.3 KB | Display | |
Data in XML | 4c13_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 4c13_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c13 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c13 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55282.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: K219 HAS BEEN MODIFIED BY CARBAMOYLATION / Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 8325 / Plasmid: PET2160 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: D4U2M7, UniProt: Q2FZP6*PLUS, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase |
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-Non-polymers , 6 types, 219 molecules
#2: Chemical | ChemComp-CL / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-UML / | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-K / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | AN ARG-SER-HIS6 ON THE C-TERMINUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.15 % / Description: NONE |
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Crystal grow | Details: MORPHEUS SCREEN CONDITION C5 (0.1 M NA HEPES/MOPS PH 7.5, 0.09 M NITRATE PHOSPHATE SULPHATE MIX, 30 % (W/V) PEG550MME/PEG20K MIX) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.7 Å / Num. obs: 44765 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.9→78.86 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.68 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→78.86 Å
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Refine LS restraints |
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